'06 Road glide Security problem

I have an '06 Road Glide with a security system that automatically shuts off the fuel pump when you turn off the bike. The battery was drained completely when the ignition switch was accidently left on overnight. The battery took a full charge the next day but the turn signals and fuel pump is not working now. I have already changed all the fuses but still can not get the bike to start. Any ideas on what might be wrong?

I think I do need to disarm the alarm system as the battery was completely dead. After reading the self help section on this site, I think I need to disarm the system. I am a little worried because the turn signals are not working either but if I understand correctly they are a part of the security system, right? Thanks for your help.